[gmx-users] timestep

David van der Spoel spoel at xray.bmc.uu.se
Mon Mar 25 19:32:09 CET 2002

On Mon, 25 Mar 2002, Anton Feenstra wrote:

>Rainer Boeckmann wrote:
>> maybe that's the problem. I did in fact only change the timestep. But: how do
>> parameters like nstlist affect the energies at step 0? The kinetic energy at step
>> 0 is different fot two runs starting from the same gro-file but with different
>> delta t. Thought these parameters were only important for later steps...
>> Thanks a lot,
>I can't see any relation between nstlist and properties at step 0,
>but dt will actually affect these. The reason is that in the trajectory
>(or .gro file) coordinates are stored at whole time steps and velocities
>at half. Changing the timestep will change the 'interval' between the
>time of the velocities and the coordinates. This might give rise to some
There is one relation: initial shake.

Groeten, David.
Dr. David van der Spoel, 	Biomedical center, Dept. of Biochemistry
Husargatan 3, Box 576,  	75123 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://zorn.bmc.uu.se/~spoel

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